LAMMPS (23 Jun 2022)
# replicate water box with AMOEBA or HIPPO

units           real
boundary        p p p

atom_style      amoeba
bond_style      class2
angle_style     amoeba
dihedral_style  none

# per-atom properties required by AMOEBA or HIPPO

fix             amtype all property/atom i_amtype ghost yes
fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
fix             extra2 all property/atom i_polaxe d2_xyzaxis 3

# read data file

read_data       data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
  orthogonal box = (0 0 0) to (18.643 18.643 18.643)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  648 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  432 bonds
  reading angles ...
  216 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.010 seconds

# force field

pair_style      amoeba
pair_coeff      * * amoeba_water.prm amoeba_water_box.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water_box.key with DATE: 2022-07-05

special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0.5      0.5      0.5     
  special bond factors coul:  0.5      0.5      0.5     
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of 1-5 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.001 seconds

# thermo output

compute         virial all pressure NULL virial

thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]

#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify     1 sort id

# dynamics

fix             1 all nve

thermo          10
run             100
AMOEBA force field settings
  hal: cut 7 taper 6 vscale 0 0 1 1
  multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
  polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
  precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9
  ghost atom cutoff = 9
  binsize = 4.5, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair amoeba, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  AMOEBA group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
         0   0             -2172.0637      166.82637      83.732524      0              0              250.5589      -1921.5048     -6181.4178     -4772.1682     -6954.8414     -6817.2437     -272.19967      3173.3481      2229.9454    
        10   105.50186     -2373.7036      136.67877      106.86833      0              0              243.5471      -1926.6873     -8440.8076     -10450.396     -9513.7369     -9664.6007     -301.7395       322.28511      1917.0314    
        20   143.89822     -2358.363       70.950306      76.775658      0              0              147.72596     -1933.1172     -7370.2083     -7728.5515     -11580.39      -8675.2341     -806.78779      780.67516      2096.34      
        30   157.22465     -2375.4739      50.393531      87.108003      0              0              137.50153     -1934.7514     -4449.577      -6946.7795     -7865.2165     -4954.2358     -417.69587     -1004.2877     -36.388669    
        40   150.92481     -2354.1892      78.482464      53.798462      0              0              132.28093     -1930.8371      353.42948     -939.14353     -4636.5062      475.58057     -1073.8523     -1583.9471     -574.21807    
        50   153.0181      -2388.7322      100.20232      65.813823      0              0              166.01614     -1927.6078      3975.1981      1368.1361      425.64533      3886.0124     -1806.8586     -2534.5272     -2118.2395    
        60   155.01494     -2364.3168      92.946192      44.248949      0              0              137.19514     -1928.1623      5793.7546      3524.7523      1420.4096      6108.7958     -1536.5261     -2558.8204     -1501.5292    
        70   166.70755     -2383.503       76.491199      55.01988       0              0              131.51108     -1930.4824      4744.1583      1919.3954      2838.7666      2669.745      -169.21643     -188.08678     -2256.4142    
        80   171.83506     -2388.0612      76.465932      49.1299        0              0              125.59583     -1931.067       2210.3658     -318.23867      330.74353     -395.26693     -43.142216      252.53012     -1987.0412    
        90   175.73401     -2423.8154      90.786573      63.719496      0              0              154.50607     -1930.3915     -916.91571     -3942.3954     -2566.5361     -3414.8202      199.82369      2365.9443     -266.38604    
       100   173.72684     -2422.367       99.75941       57.294464      0              0              157.05387     -1930.2663     -3585.8356     -5734.1341     -5882.0146     -6232.4353     -227.79935      959.68225      404.47924    
Loop time of 14.5572 on 1 procs for 100 steps with 648 atoms

Performance: 0.594 ns/day, 40.437 hours/ns, 6.869 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

AMOEBA timing breakdown:
  Init    time: 0.0224497      0.15%
  Hal     time: 1.00248        6.90%
  Mpole   time: 1.42229        9.78%
  Induce  time: 9.23983       63.55%
  Polar   time: 2.8515        19.61%
  Total   time: 14.5386     

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 14.539     | 14.539     | 14.539     |   0.0 | 99.87
Bond    | 0.0029302  | 0.0029302  | 0.0029302  |   0.0 |  0.02
Neigh   | 0.010789   | 0.010789   | 0.010789   |   0.0 |  0.07
Comm    | 0.0027888  | 0.0027888  | 0.0027888  |   0.0 |  0.02
Output  | 0.00040039 | 0.00040039 | 0.00040039 |   0.0 |  0.00
Modify  | 0.0007305  | 0.0007305  | 0.0007305  |   0.0 |  0.01
Other   |            | 0.0008703  |            |       |  0.01

Nlocal:            648 ave         648 max         648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4290 ave        4290 max        4290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          98545 ave       98545 max       98545 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 98545
Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:14
